Discovery and evaluation of novel SHIP-1 inhibitors

• Published in: Bioorganic & medicinal chemistry Vol. 114; p. 117965
• Main Authors: Miao, Jinmin, Lin, Jianping, Dong, Jiajun, Amarasinghe, Ovini, Mason, Emily R., Chu, Shaoyou, Qu, Zihan, Cullers, Clayton C., Putt, Karson S., Zhang, Zhong-Yin
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 15.11.2024
• Subjects: Alzheimer’s disease; Dose-Response Relationship, Drug; Drug Discovery; Enzyme Inhibitors - chemical synthesis; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; High-throughput screening; High-Throughput Screening Assays; Humans; Microglial phagocytosis; Molecular Structure; Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases - antagonists & inhibitors; Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases - metabolism; Src Homology 2-containing Inositol 5′-Phosphatase-1 (SHIP-1); Structure-Activity Relationship; High-throughput screening; Src Homology 2-containing Inositol 5′-Phosphatase-1 (SHIP-1); Alzheimer’s disease; Microglial phagocytosis
• ISSN: 0968-0896; 1464-3391; 1464-3391
• DOI: 10.1016/j.bmc.2024.117965

[Display omitted] •A high-throughput screening platform was implemented to explore SHIP-1 modulators.•Three novel SHIP-1 inhibitor scaffolds with low µM IC50s were identified.•SP3-12 inhibits SHIP-1 with a Ki of 3.2 µM and a 7-fold selectivity over SHIP-2.•SP3-12 activates phagocytosis in human microglial cells with an EC50 of 2.0 µM. Src Homology 2-containing Inositol 5′-Phosphatase-1 (SHIP-1), encoded by INPP5D, has been identified as an Alzheimer’s disease (AD) risk-associated gene through recent genetic and epigenetic studies. SHIP-1 confers AD risk by inhibiting the TREM2 cascade and reducing beneficial microglial cellular processes, including phagocytosis. While several small molecules have been reported to modulate SHIP-1 activity, their limited selectivity and efficacy in advanced models restricted their potential as therapeutic agents or probes for biological studies. Herein, we validated and implemented a high-throughput screening platform to explore new chemotypes that can modulate the phosphatase activity of SHIP-1. We screened 49,260 central nervous system (CNS)-penetrate compounds sourced from commercial vendors using the malachite green-based assay for anti-SHIP-1 activity. Through analysis, prioritization, and validation of the screening hits, we identified three novel types of scaffolds that inhibit the SHIP-1 phosphatase activity with IC50s as low as 46.6 µM. To improve the inhibitory activity of these promising hits, we carried out structure–activity relationship (SAR) studies, resulting in a lead molecule SP3-12 that inhibits SHIP-1 with an IC50 value of 6.1 μM. Kinetic analyses of SP3-12 revealed that its inhibition mechanism is competitive, with a Ki value of 3.2 µM for SHIP-1 and a 7-fold selectivity over SHIP-2. Furthermore, results from testing in a microglial phagocytosis/cell health high content assay indicated that SP3-12 could effectively activate phagocytosis in human microglial clone 3 (HMC3) cells, with an EC50 of 2.0 µM, without cytotoxicity in the dose range. Given its potency, selectivity, and cellular activity, SP3-12 emerges as a promising small molecule inhibitor with potential for investigating the biological functions of SHIP-1.